Table 2. Summary of detected regions on NGS data sets.
| Methods | RUBIC | GISTIC2 |
|---|---|---|
| BRCA (lcWGS; n=90) | ||
| No. regions (gains/losses) | 80/43 | 26/29 |
| No. Census regions (gains/losses) | 47/10 | 17/7 |
| No. Census genes (gains/losses) | 90/21 | 25/20 |
| No. bona fide genes (52 oncogenes/12 tumour suppressors) | 32/3 | 10/2 |
| Enrichment P values for bona fide genes | 2 × 10−4/0.022 | <1 × 10−4/0.083 |
| Avg. driver density (gains/losses) | 0.12/0.24 | 0.09/0.13 |
| Region overlap with SNP6 | 0.50/0.42 | 0.42/0.33 |
| BRCA (WES; n=383) | ||
| No. regions (gains/losses) | 46/9 | 13/3 |
| No. Census regions (gains/losses) | 32/4 | 10/1 |
| No. Census genes (gains/losses) | 58/14 | 16/1 |
| No. bona fide genes (52 oncogenes/12 tumour suppressors) | 28/2 | 10/1 |
| Enrichment P values for bona fide genes | <1 × 10−4/0.018 | <1 × 10−4/0.021 |
| Avg. driver density (gains/losses) | 0.07/0.25 | 0.08/0.21 |
| Region overlap with SNP6 | 0.87/0.56 | 0.61/0.33 |
Recurrent copy number regions predicted by RUBIC and GISTIC2 for BRCA data sets derived from low coverage whole-genome sequencing (lcWGS) and TCGA WES. For each subtable containing the results of a specific sequencing platform the rows represent the following: the first row (labelled ‘no. regions') represents the total number of focal recurrent regions detected by each algorithm. The second row shows the number of regions that overlap with Census genes. The third row represents the total number of Census genes detected. The fourth row shows the number of BRCA bona fide oncogenes/tumour suppressors detected. The fifth row shows the enrichment P values for bona-fide drivers in regions based on a cyclic permutation test. The sixth row shows the average driver density in the called regions. The final row shows the proportion of regions detected in NGS data that overlap with regions found for the SNP6 TCGA data set. Each entry has two values (separated with a slash) representing recurrent gains and losses, respectively.